Structure of PDB 5vmt Chain D Binding Site BS01

Receptor Information
>5vmt Chain D (length=334) Species: 521006 (Neisseria gonorrhoeae NCCP11945) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMSIKVAINGFGRIGRLALRQIEKAHGIEVAAVNDLTPAEMLLHLFKYDS
TQGRFQGTAELKDDAIVVNGREIKVFANPNPEELPWGELGVDVVLECTGF
FTNKTKAEAHIRAGARKVVISAPGGNDVKTVVYGVNQDILDGSETVISAA
SCTTNCLAPMAAVLQKEFGVVEGLMTTIHAYTGDQNTLDAPHRKGDLRRA
RAAALNIVPNSTGAAKAIGLVIPELNGKLDGSAQRVPVATGSLTELVSVL
ERPATKEEINAAMKAASSESYGYNEDQIVSSDVVGIEYGSLFDATQTRVM
TVGGKQLVKTVAWYDNEMSYTCQLVRTLEYFAGK
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5vmt Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5vmt Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G11 R12 I13 D34 L35 P78 C96 T97 G98 F99 S120 C151 N315 Y319
Binding residue
(residue number reindexed from 1)		G12 R13 I14 D35 L36 P79 C97 T98 G99 F100 S121 C152 N316 Y320
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C151 H178
Catalytic site (residue number reindexed from 1) C152 H179
Enzyme Commision number 1.2.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006006 glucose metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vmt, PDBe:5vmt, PDBj:5vmt
PDBsum5vmt
PubMed31930578
UniProtB4RPP8

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